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@@ -1,64 +1,64 @@
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- # Description
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-This repository contains the full data set for constructing the DAPI template, the full DAPI template creation pipeline and the automatic slice segmentation.
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-
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-# Automatic slice segmentation
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-
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-Program for automatic segmentation to a DAPI-stained coronal mouse brain slices.
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-
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-
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-## Dependencies
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-* Python 3.6
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-* Ants (https://github.com/ANTsX/ANTs)
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-* Various python packages detailed in requirements.txt
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-
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-## Prerequisites
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-* A high-resolution, DAPI modality TIFF image of a brain slice. Can have multiple channels.
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-* A template file (.nii or .nii.gz)
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-* A segmentation of the template file (.nii or .nii.gz)
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-
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-## Usage
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-* Use preprocess.py to prepare input slice for automatic registration
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-* Use auto_seg.py with preprocessed slice which will output a folder containing segmentation registered to slice.
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-
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-## auto_seg.py
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-**Usage**
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-```sh
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-python3 auto_seg.py sliceloc segloc templateloc --bregma [coord]
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-```
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-**Positional/Required Arguments**
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-
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-|||
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-|--------------------------------|-----------------------------|
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-|`sliceloc` |Location of the slice you wish to register (.nii or.nii.gz) |
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-|`segloc` |Location of file containing segmentation of the template (.nii or.nii.gz) |
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-|`templateloc`|Location of template file (.nii or .nii.gz)|
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-|`--bregma [coord]`|Bregma coordinate of input slice (if --approx argument is present, this is an optional argument)|
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-
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-**Optional arguments**
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-
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-| | |
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-|---|---|
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-|`--approx [index]` |Provide the location of the slice as a z-index of the template. Can be used instead of --bregma argument.|
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-|`--out [directory]` |Provide an alternative output directory (default directory is /output) |
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-|`--dapi [index]` |Index of the DAPI channel in the slice, by default the DAPI channel is assumed to be the last channel|
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-
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-## preprocess.py
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-**Usage**
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-```sh
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-python3 preprocess.py file dir -s Series -b [True/False] --pdim [pixeldimension]
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-```
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-**Positional/Required Arguments**
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-
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-|||
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-|--------------------------------|-----------------------------|
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-|`file` |Location of the file to be preprocessed (.tiff or .nd2) |
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-|`dir` |Directory to output preprocessed files (will output .nii files)|
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-|`-s`|The series to extract (If input file is single-series, use 0 for this argument)|
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-
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-**Optional arguments**
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-
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-|||
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-|--------------------------------|-----------------------------|
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-|`--b [True/False]` |Bias field correction: Whether to use bias-field correction in preprocessing (default: True)|
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-|`--pdim [pixeldimensions]` |Dimensions of pixels, if not provided, these will be extracted from image metadata|
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-
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+ # Description
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+This repository contains the full data set for constructing the DAPI template, the full DAPI template creation pipeline and the automatic slice segmentation.
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+
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+# Automatic slice segmentation
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|
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+
|
|
|
+Program for automatic segmentation to a DAPI-stained coronal mouse brain slices.
|
|
|
+
|
|
|
+
|
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+## Dependencies
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+* Python 3.6
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+* Ants (https://github.com/ANTsX/ANTs)
|
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+* Various python packages detailed in requirements.txt
|
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+
|
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+## Prerequisites
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|
+* A high-resolution, DAPI modality TIFF image of a brain slice. Can have multiple channels.
|
|
|
+* A template file (.nii or .nii.gz)
|
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+* A segmentation of the template file (.nii or .nii.gz)
|
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+
|
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+## Usage
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+* Use preprocess.py to prepare input slice for automatic registration
|
|
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+* Use auto_seg.py with preprocessed slice which will output a folder containing segmentation registered to slice.
|
|
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+
|
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+## auto_seg.py
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+**Usage**
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+```sh
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+python3 auto_seg.py sliceloc segloc templateloc --bregma [coord]
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+```
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+**Positional/Required Arguments**
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+
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+|||
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+|--------------------------------|-----------------------------|
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+|`sliceloc` |Location of the slice you wish to register (.nii or.nii.gz) |
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+|`segloc` |Location of file containing segmentation of the template (.nii or.nii.gz) |
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+|`templateloc`|Location of template file (.nii or .nii.gz)|
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+|`--bregma [coord]`|Bregma coordinate of input slice (if --approx argument is present, this is an optional argument)|
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+
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+**Optional arguments**
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+
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+| | |
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+|---|---|
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+|`--approx [index]` |Provide the location of the slice as a z-index of the template. Can be used instead of --bregma argument.|
|
|
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+|`--out [directory]` |Provide an alternative output directory (default directory is /output) |
|
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+|`--dapi [index]` |Index of the DAPI channel in the slice, by default the DAPI channel is assumed to be the last channel|
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+
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+## preprocess.py
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+**Usage**
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+```sh
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+python3 preprocess.py file dir -s Series -b [True/False] --pdim [pixeldimension]
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+```
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+**Positional/Required Arguments**
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+
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+|||
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+|--------------------------------|-----------------------------|
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+|`file` |Location of the file to be preprocessed (.tiff or .nd2) |
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+|`dir` |Directory to output preprocessed files (will output .nii files)|
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+|`-s`|The series to extract (If input file is single-series, use 0 for this argument)|
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+
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+**Optional arguments**
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+
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+|||
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+|--------------------------------|-----------------------------|
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+|`--b [True/False]` |Bias field correction: Whether to use bias-field correction in preprocessing (default: True)|
|
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+|`--pdim [pixeldimensions]` |Dimensions of pixels, if not provided, these will be extracted from image metadata|
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+
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